EoE Transcriptome by RNA Sequencing (2014)

Primary publication:
Sherrill et al, 2014
https://doi.org/10.1038/gene.2014.27

Experimental Design:

RNA sequencing was performed to quantify transcripts present in esophageal biopsy specimens obtained from 6 healthy controls (Control) and 10 patients with active EoE (EoE).

Kinetics of esophageal epithelial cell line (TE-7) transcriptional response to IL-13

Primary publication:
Rochman et al, 2014
https://doi.org/10.1038/mi.2014.109

Experimental Design:

TE-7 cells (a human esophageal epithelial cell line) were stimulated with IL-13 (100 ng/ml) for 2h, 6h, or 24h. Transcript levels were quantified by RNA sequencing. Untreated cells (Control_2h, Control_4h, Control_24h); IL-13-treated cells (IL-13_2h, IL-13_6h, IL-13_24h).

Gene expression of undifferentiated EPC2 (monolayer), differentiated EPC2 (ALI), and differentiated SPINK7-silenced EPC2 (ALI)

Primary publication:
Azouz et al, 2018
https://doi.org/10.1126/scitranslmed.aap9736

Experimental Design:

A telomerase-immortalized human esophageal epithelial cell line (EPC2 cells) was transfected with either non-silencing control shRNA or SPINK7 shRNA. Cells were grown either in monolayer culture (undifferentiated) or in air liquid interface (ALI) cultures (differentiated). Transcript levels of the following types of cells were determined: cells transfected with non-silencing control shRNA and grown in monolayer culture (Undif_NSC); cells transfected with non-silencing control shRNA grown at the ALI (NSC); cells transfected with SPINK7 shRNA grown at the ALI (SPINK7_silenced).

Gene expression of undifferentiated EPC2 (monolayer), differentiated EPC2 (ALI), and differentiated EPC2 (ALI) +/- IL-13

Primary publication:
Sherrill et al, 2014
https://doi.org/10.1038/mi.2013.90

Experimental Design:

A telomerase-immortalized human esophageal epithelial cell line (EPC2 cells) was grown submerged in monolayer culture (undifferentiated) for 8 days, or were grown submerged in monolayer culture for 8 days followed by 6 days of culture at the air liquid interface (differentiated). In some cases, cells were treated with IL-13 (100 ng/ml) during the 6 days of ALI culture. Transcript levels of the following conditions were assessed by RNA sequencing: Day_0: cells grown submerged for 8 days; Day_6: cells grown submerged for 8 days and then grown at the ALI for 6 additional days; Day_6_IL-13: cells grown submerged for 8 days and then grown at the ALI for 6 additional days in the presence of IL-13.

Esophageal Gene Expression (2006)

Primary publication:
Blanchard et al, 2006
https://doi.org/10.1172/JCI26679
Blanchard et al, 2007
https://doi.org/10.1016/j.jaci.2007.10.024
Caldwell et al, 2010
https://doi.org/10.1016/j.jaci.2010.01.038

Experimental Design:

RNA isolated from distal esophageal tissue was subjected to genome-wide transcript profile microarray analysis. Experimental groups: NL: control; CE: chronic esophagitis; EoE: active EoE; EoE+FP+R: fluticasone responder; EoE+FP+NR: fluticasone non-responder.

Gastric Gene Expression (2014)

Primary publication:
Caldwell et al, 2014
https://doi.org/10.1016/j.jaci.2014.07.026

Experimental Design:

RNA isolated from gastric antrum tissue was subjected to genome-wide transcript analysis by microarray analysis. Experimental groups: control and active eosinophilic gastritis (EG).

Transcriptional response of primary esophageal epithelial cells to IL-13

Primary publication:
Caldwell et al, 2014
https://doi.org/10.1016/j.jaci.2007.10.024

Experimental Design:

Human primary esophageal epithelial cells from patients with EoE were cultured in the presence or absence of IL-13 (100 ng/ml) for 48 h, and the mRNA was subjected to genome-wide transcript profile microarray analysis. The data from the IL-13-stimulated cells were normalized pairwise to unstimulated controls.

EoE Diagnostic Panel: EoE Endotypes

Primary publication:
Shoda et al, 2018
https://doi.org/10.1016/S2468-1253(18)30096-7

Experimental Design:

RNA was isolated from distal esophageal tissue of 86 individuals with active EoE. The RNA was subjected to EDP analysis, which quantifies 96 individual gene transcripts. Graphs depict the -deltaCt value -(ct of GAPDH – ct of gene of interest) for each individual. Experimental groups: EoEe1: EoE endotype 1; EoEe2: EoE endotype 2; EoEe3: EoE endotype 3.

Single cell RNA sequencing of T-cells

Primary publication:
Wen et al, 2019
https://doi.org/10.1172/JCI125917

Experimental Design:

Single-cell transcriptome profililng of esophagus biopsies from patients with active eosinophilic esophagitis (EoE, n=11), in remission (n=6), and without disease (n=5).

Gene expression profiling of bone marrow and esophagus from PIR-B KO mice by microarray (2016)

Primary publication:
Ben Baruch-Morgenstern et al, 2016
https://doi.org/10.4049/jimmunol.1501873

Experimental Design:

17 samples were analyzed in this experiment. The experiment was designed with 3 replicates for each treatment/genotype/tissue (Dox and no Dox/wildtype and knockout/bone marrow and esophagus), with the exception of the sample wildtype bone marrow no Dox where 1 replicate was dropped due to low hybridization signal. The no Dox and wildtype samples are controls for the treatment and background of the mice. Experimental groups: bm_WT_noDox: bone marrow, wildtype, no Dox; bm_KO_noDox: bone marrow, PirB knockout, no Dox; bm_WT_Dox: bone marrow, wildtype, Dox; bm_KO_Dox: bone marrow, PirB knockout, Dox; eso_WT_Dox: esophagus, wildtype, Dox; eso_KO_Dox: esophagus, PirB knockout, Dox.

EG Transcriptome by RNA Sequencing

Experimental Design:

RNA sequencing was performed to quantify transcripts present in gastric biopsy specimens obtained from 12 healthy controls (Non-EG) and 9 patients with EG (EG).

Mouse Eosinophils +/- IL4 or IL33

Experimental Design:

RNA sequencing was performed to quantify transcripts present in LDBM Mouse Eosinophils untreated, treated with IL-4, or treated with IL-33 at 1 hour and 4 hours.

Effect of PPIs omeprazole and esomeprazole on gene expression in EPC2 cells

EPC2 +/- PPI Multiplex